Nucleic acids involved in viral infection

ABSTRACT

The invention provides isolated viral and human nucleic acids associated with viral infection and various nucleic acid molecules relating thereto or derived therefrom. The nucleic acids are useful for prevention, treatment and diagnosis of viral infections.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional App. No.60/868,666, filed Dec. 5, 2006 and U.S. Provisional App. No. 60/971,265,filed Sep. 11, 2007, the contents each of which are incorporated hereinby reference.

FIELD OF THE INVENTION

Described herein are viral and host microRNA molecules associated withviral infections, as well as various nucleic acid molecules relatingthereto or derived therefrom.

BACKGROUND OF THE INVENTION

MicroRNAs (miRNAs) are a family of 18-24 nucleotide long non-codingsmall RNAs, that suppress translation of target genes by binding totheir mRNA, thereby regulating the expression of at least 30% of allhuman genes. Although miRNAs are present in a wide range of speciesincluding C. elegans, Drosophila and humans, they have only recentlybeen identified. More importantly, the role of miRNAs in the developmentand progression of disease has only recently become appreciated. Thereare currently about 500 known human microRNAs, and their number probablyexceeds 800.

As a result of their small size, miRNAs have been difficult to identifyusing standard methodologies. A limited number of miRNAs have beenidentified by extracting large quantities of RNA. miRNAs have beenidentified that contribute to the presentation of visibly discernablephenotypes. Expression array data show that miRNAs are expressed indifferent developmental stages or in different tissues. The restrictionof miRNAs to certain tissues or at limited developmental stagesindicates that the miRNAs identified to date are likely only a smallfraction of the total miRNAs.

Computational approaches have recently been developed to identify theremainder of miRNAs in the genome. Tools such as MiRscan and MiRseekerhave identified miRNAs that were later experimentally confirmed. Basedon the fundamental importance of miRNAs in mammalian biology anddisease, the art needs to identify unknown miRNAs.

Viruses can establish a variety of types of infection. These infectionscan be generally classified as lytic or persistent, though some lyticinfections are considered persistent. Generally, persistent infectionsfall into two categories: (1) chronic (productive) infection, i.e.,infection wherein infectious virus is present and can be recovered bytraditional biological methods and (2) latent infection, i.e., infectionwherein viral genome is present in the cell but infectious virus isgenerally not produced except during intermittent episodes ofreactivation. Persistence generally involves stages of both productiveand latent infection.

Lytic infections can also persist under conditions where only a smallfraction of the total cells are infected (smoldering (cycling)infection). The few infected cells release virus and are killed, but theprogeny virus again only infect a small number of the total cells.

Traditional treatments for viral infection include pharmaceuticals aimedat specific virus derived proteins, or recombinant (cloned) immunemodulators (host derived), such as the interferons. However, the currentmethods have several limitations and drawbacks which include high ratesof viral mutations which render anti-viral pharmaceuticals ineffective.For immune modulators, limited effectiveness, limiting side effects, alack of specificity all limit the general applicability of these agents.Also the rate of success with current antivirals and immune-modulatorshas been disappointing.

Viral infections are a continuing medical problem because, like anyrapidly-dividing infectious agent, there are continuing mutations thathelp some sub-populations of viruses continue to be resistant to currenttreatment regimens. Many virally-based diseases do not have effectiveanti-viral treatments, because such treatments address the symptoms ofthe viral disease and not the root cause of the disease. There is a needin the art to discover and develop new anti-viral therapies.

SUMMARY OF THE INVENTION

Provided herein are compositions and methods for the identification,suppression and modulation of viral infection in a target cell. Alsoprovided are pharmaceutical compositions and kits for use in practicingthe methods. The compositions and methods may be used in a variety ofapplications, including the treatment of subjects suffering from a viralmediated disease condition.

Also provided is an isolated nucleic acid comprising a sequence selectedfrom the group consisting of SEQ ID NOS: 1-9,221, 15,366-15,392 and15,516-15,527; the complementary sequence thereof; and a sequence atleast about 80% identical thereto. The nucleic acid may be from 5-250nucleotides in length. The nucleic acid may comprise a modified base.

Further provided is a probe comprising the nucleic acid. The probe maycomprise at least 8-22 contiguous nucleotides complementary to SEQ IDNOS: 1-9,221, 15,366-15,392 and 15,516-15,527, or a variant thereof. Theprobe may also comprise at least 8-22 contiguous nucleotidescomplementary to a host microRNA differentially expressed in viralinfection, or a variant thereof.

Also provided is a composition comprising the nucleic acid.

Further provided is a biochip comprising the nucleic acid.

Also provided is a vector comprising the nucleic acid.

Further provided is a host cell comprising the nucleic acid.

Also provided is a pharmaceutical composition comprising the nucleicacid as an active ingredient, and a composition comprising the vector.

Further provided is a method of preventing or treating viral infectionor a condition associated with a viral infection in a subject in needthereof. The method may comprise administering to the subject aneffective amount of a.composition comprising a nucleic acid sequenceselected from the group consisting of SEQ ID NOS: 1-9,221, 15,366-15,392and 15,516-15,527; a complementary sequence thereof; and a sequence atleast about 80% identical thereto. The viral infection may be caused bya virus selected from the group consisting of: HSV1, HSV2, RSV, EBV,Influenza A, HCV, HPV, HIV, HBV and Vaccinia virus. The conditionassociated with the viral infection may be selected from the groupconsisting of: Burkitt's lymphoma, nasopharingal carcinoma, ovariancarcinoma, cervical cancer, hepatitis, mononucleosis, genital herpes,encephalitis, influenza and bronchiolitis.

Also provided is a method for reducing the amount of virus replicationin a target cell, where the target cell may be present in vitro or invivo.

Further provided is the use of a nucleic acid comprising a nucleic acidsequence selected from the group consisting of SEQ ID NOS: 1-9,221,15,366-15,392 and 15,516-15,527; a complementary sequence thereof; and asequence at least about 80% identical thereto for the manufacture of amedicament for the treatment or prevention of viral infection.

Also provided is a method for modulating a nucleic acid. The method maycomprise modulating a first nucleic acid comprising the nucleotidesequence selected from the group consisting of (a) any one of SEQ IDNOS: 9,222-15,365 and 15,393-15,515, (b) a complementary sequence of(a), and (c) sequence at least about 80% identical to (a) or (b).

The method may further comprise introducing a second nucleic acid to thefirst nucleic acid wherein the second nucleic acid is selected from thegroup consisting of (a) SEQ ID NOS: 1-9,221, 15,366-15,392,15,516-15,527, and (b) sequence at least about 80% identical to (a),wherein the second nucleic acid modulates expression of the firstnucleic acid. The first nucleic acid may be a miRNA target-gene. Thesecond nucleic acid may be a miRNA or siRNA.

Further provided is a method of inhibiting expression of a target genein a cell. A nucleic acid may be introduced into the cell in an amountsufficient to inhibit expression of the target gene. The target gene maycomprise a binding site substantially identical to SEQ ID NOS:9,222-15,365 and 15,393-15,515, or a variant thereof. The nucleic acidmay comprise a portion of SEQ ID NOS: 1-9,221, 15,366-15,392 and15,516-15,527 or a variant thereof. Expression of a target gene may beinhibited in vitro or in vivo.

Also provided is a method of detecting viral infection of a cellcomprising determining the expression level of a nucleic acid sequenceselected from the group consisting of SEQ ID NOS: 1-9,221, 15,366-15,392and 15,516-15,527; a complementary sequence thereto or a sequence atleast about 80% identical thereto. The method of detecting viralinfection may comprise a microRNA array, RT-PCR, or Northern blotanalysis.

Further provided is a kit comprising the nucleic acid.

Also provided is a method of reducing the amount of virus replication ina target cell, which may comprise introducing an effective amount of acomposition into a target cell infected with a virus. The compositionmay comprise a nucleic acid sequence selected from the group consistingof SEQ ID NOS: 1-9,221, 15,366-15,392 and 15,516-15,527; a complementarysequence thereof; and a sequence at least about 80% identical thereto.The target cell may be in vitro or in vivo. A subject may comprise saidtarget cell. The virus may be HSV1, HSV2, RSV, EBV, Influenza A, HCV,HPV, HIV, HBV, or Vaccinia virus. The method may be used to treat aviral mediated disease condition in a subject in need thereof. Thedisease condition may be Burkitt's lymphoma, nasopharingal carcinoma,ovarian carcinoma, cervical cancer, hepatitis, mononucleosis, influenza,genital herpes, encephalitis, or bronchiolitis.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows microRNA expression profiling of respiratory syncytialvirus (RSV) infected HEp2 cells as compared to uninfected control cellsusing miRdicator™ microRNA array. The expressed host microRNA AMB-10594(SEQ ID NO: 15,374) is indicated.

FIGS. 2A-2B show microRNA expression profiling of MDCK cells infectedwith Influenza A (FluA) as compared to uninfected control cells usingmiRdicator™ microRNA array. The expressed microRNA of FluA-12 (SEQ IDNO: 15,378) is circled. Two independent experiments are shown.

FIG. 3 shows microRNA expression profiling of herpes simplex virus typel(HSV1) microRNAs in Vero cells infected with HSV1 and HSV2 as comparedto uninfected control cells. The expressed microRNA HSV1-miR-H1 (SEQ IDNO: 15,375) is indicated.

FIG. 4 shows microRNA expression profiling of HSV2 microRNAs in Verocells infected with HSV2. The expressed microRNAs: HSV2-Pred13 (SEQ IDNO: 15,376) and HSV2-8 (SEQ ID NO: 15,377) are indicated.

FIGS. 5A-5B show up-regulation of host microRNA AMB-10594 (SEQ ID NO:15,374) (circled) following various viral infections of various cells:RSV infected HEp2 cells (FIG. 5A), HSV2 infected HF cells (FIG. 5B),HSV1 infected HF cells (FIG. 5D), and following interferon treatment ofHF cells (FIG. 5C).

FIG. 6 shows Northern blot analysis of hsa-miR-181a (SEQ ID NO: 15,366)differentially expressed in HEp2 uninfected (−) and RSV infected cells.

FIGS. 7A-7B show real time PCR analysis of HSV2 microRNA-pred-13 (SEQ IDNO: 15,376), HSV2 microRNA-8 (SEQ ID NO: 15,377) and their bulge.

FIG. 8 shows higher expression of hsa-mir-21 (SEQ ID NO: 15,373) in Verocells infected with HSV1 in comparison with HSV2 infected cells.

FIG. 9 shows Northern blot analysis of HSV2 microRNA-pred-13 (SEQ ID NO:15,376). The lower part of the figure depicts Ethidium Bromide stainingof the gel.

FIG. 10 shows Northern blot analysis of HSV2 microRNA-8 (SEQ ID NO:15,377). The lower part of the figure depicts Ethidium Bromide stainingof the gel.

FIG. 11 shows the results of quantitative RT-PCR of EBV viral load inB95-8 cells transfected with EBV anti-mir oligonucleotides. B95-8 cellspersistently infected with EBV were transfected with various antagonists(2-O-Methyl antimir oligonucleotides, SEQ ID NOs: 15,517, 15,519,15,521, 15,523, 15,525, and 15,527) to EBV microRNAs. After 120 hrs,cells were harvested, DNA was extracted, and EBV DNA copies/ml wasdetermined by qRTPCR, using commercial standards for EBV viral load.

DETAILED DESCRIPTION

During viral infection, viruses express specific miRNAs and alter hostmiRNA expression. Provided herein are compositions and methods toprevent or treat viral infection. Identification of specific miRNAsignatures and the targets of these miRNAs induced by viruses may beused to identify cellulai and viral genes required for viral infection.

The inventors have made the surprising discovery that the expressionlevels of several viral microRNAs (SEQ ID NOS: 15,375-15,387) and hostmicroRNAs (SEQ ID NOS: 15,366-15,374) were altered following viralinfection. Furthermore, different viruses produce distinct microRNAsexpression patterns in various viral infected cells.

Specific viral and host miRNA nucleic acids may be used as noveltherapeutics in the treatment of viral infections. The nucleic acidsalso be used in diagnostics for clinical and research settings includingdetection of latent infections. The disclosed viral and host miRNAs maybe used to discover new cellular and viral drugs and drug targets.

Described herein is the expression of viral and host encoded microRNAsin viral infections by HSV1, HSV2, RSV, EBV, Influenza A, HCV, HPV andVaccinia viruses.

Provided herein are nucleotide sequences of viral, and human miRNAs,precursors thereto, targets thereof and related sequences. Such nucleicacids may be used for diagnostic purposes, therapeutic purposes, andalso for modifying target gene expression.

1. Definitions

Before the present compositions and methods are disclosed and described,it is to be understood that the terminology used herein is for thepurpose of describing particular embodiments only and is not intended tobe limiting. It must be noted that, as used in the specification and theappended claims, the singular forms “a,” “an” and “the” include pluralreferents unless the context clearly dictates otherwise. It must furtherbe noted that the terms “and” and “or” may encompass both conjunctiveand disjunctive meaning unless the context clearly dictates otherwise.

For the recitation of numeric ranges herein, each intervening numberthere between with the same degree of precision is explicitlycontemplated. For example, for the range of 6-9, the numbers 7 and 8 arecontemplated in addition to 6 and 9, and for the range 6.0-7.0, thenumbers 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6, 6.7, 6.8, 6.9, and 7.0 areexplicitly contemplated.

“Animal” as used herein may mean fish, amphibians, reptiles, birds, andmammals, such as mice, rats, rabbits, goats, cats, dogs, cows, apes andhumans.

“Attached” or “immobilized” as used herein to refer to a probe and asolid support may mean that the binding between the probe and the solidsupport is sufficient to be stable under conditions of binding, washing,analysis, and removal. The binding may be covalent or non-covalent.Covalent bonds may be formed directly between the probe and the solidsupport or may be formed by a cross linker or by inclusion of a specificreactive group on either the solid support or the probe or bothmolecules. Non-covalent binding may be one or more of electrostatic,hydrophilic, and hydrophobic interactions. Included in non-covalentbinding is the covalent attachment of a molecule, such as streptavidin,to the support and the non-covalent binding of a biotinylated probe tothe streptavidin. Immobilization may also involve a combination ofcovalent and non-covalent interactions.

“Biological sample” as used herein may mean a sample of biologicaltissue or fluid that comprises nucleic acids. Such samples include, butare not limited to, tissue isolated from animals. Biological samples mayalso include sections of tissues such as biopsy and autopsy samples,frozen sections taken for histological purposes, blood, plasma, serum,sputum, stool, tears, mucus, urine, effusions, amniotic fluid, asciticfluid, hair, and skin. Biological samples also include explants andprimary and/or transformed cell cultures derived from patient tissues. Abiological sample may be provided by removing a sample of cells from ananimal, but can also be accomplished by using previously isolated cells(e.g., isolated by another person, at another time, and/or for anotherpurpose), or by performing the methods described herein in vivo.Archival tissues, such as those having treatment or outcome history, mayalso be used.

“Complement” or “complementary” as used herein may mean Watson-Crick(e.g., A-T/U and C-G) or Hoogsteen base pairing between nucleotides ornucleotide analogs of nucleic acid molecules. A complement may beidentical in length to a nucleic acid disclosed herein.

“Differential expression” may mean qualitative or quantitativedifferences in the temporal and/or cellular gene expression patternswithin and among cells and tissue. Thus, a differentially expressed genecan qualitatively have its expression altered, including an activationor inactivation, in, e.g., normal versus disease tissue. Genes may beturned on or turned off in a particular state, relative to another statethus permitting comparison of two or more states. A qualitativelyregulated gene will exhibit an expression pattern within a state or celltype that may be detectable by standard techniques. Some genes will beexpressed in one state or cell type, but not in both. Alternatively, thedifference in expression may be quantitative, e.g., in that expressionis modulated, up-regulated, resulting in an increased amount oftranscript, or down-regulated, resulting in a decreased amount oftranscript. The degree to which expression differs need only be largeenough to quantify via standard characterization techniques such asexpression arrays, quantitative reverse transcriptase PCR, northernanalysis, and RNase protection.

“Expression profile” as used herein may mean a genomic expressionprofile, e.g., an expression profile of microRNAs. Profiles may begenerated by any convenient means for determining a level of a nucleicacid sequence e.g. quantitative hybridization of microRNA, labeledmicroRNA, amplified microRNA, cRNA, etc., quantitative PCR, ELISA forquantitation, and the like, and allow the analysis of differential geneexpression between two samples. A subject or patient tumor sample, e.g.,cells or collections thereof, e.g., tissues, is assayed. Samples arecollected by any convenient method, as known in the art. Nucleic acidsequences of interest are nucleic acid sequences that are found to bepredictive, including the nucleic acid sequences provided above, wherethe expression profile may include expression data for 5, 10, 20, 25,50, 100 or more of, including all of the listed nucleic acid sequences.The term “expression profile” may also mean measuring the abundance ofthe nucleic acid sequences in the measured samples.

“Gene” used herein may be a genomic gene comprising transcriptionaland/or translational regulatory sequences and/or a coding region and/ornon-translated sequences (e.g., introns, 5′- and 3′-untranslatedsequences). The coding region of a gene may be a nucleotide sequencecoding for an amino acid sequence or a functional RNA, such as tRNA,rRNA, catalytic RNA, siRNA, miRNA and antisense RNA. A gene may also bean miRNA or cDNA corresponding to the coding regions (e.g., exons andmiRNA) optionally comprising 5′- or 3′-untranslated sequences linkedthereto. A gene may also be an amplified nucleic acid molecule producedin vitro comprising all or a part of the coding region and/or 5′- or3′-untranslated sequences linked thereto.

“Host cell” used herein may mean a naturally occurring cell or atransformed cell that may contain a vector and may support thereplication of the vector. Host cells may be cultured cells, explants,cells in vivo, and the like. Host cells may be prokaryotic cells such asE. coli, or eukaryotic cells such as yeast, insect, amphibian, ormammalian cells, such as CHO, HeLa.

“Identical” or “identity” used herein in the context of two or morenucleic acids or polypeptide sequences, may mean that the sequences havea specified percentage of residues that are the same over a specifiedregion. The percentage may be calculated by comparing optimally aligningthe two sequences, comparing the two sequences over the specifiedregion, determining the number of positions at which the identicalresidue occurs in both sequences to yield the number of matchedpositions, dividing the number of matched positions by the total numberof positions in the specified region, and multiplying the result by 100to yield the percentage of sequence identity. In cases where the twosequences are of different lengths or the alignment produces staggeredends and the specified region of comparison includes only a singlesequence, the residues of single sequence are included in thedenominator but not the numerator of the calculation. When comparing DNAand RNA, thymine (T) and uracil (U) are considered equivalent. Identitymay be performed manually or by using computer sequence algorithm suchas BLAST or BLAST 2.0.

“Inhibit” as used herein may mean prevent, suppress, repress, reduce oreliminate.

“Label” as used herein may mean a composition detectable byspectroscopic, photochemical, biochemical, immunochemical, chemical, orother physical means. For example, useful labels include P³²,fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonlyused in an ELISA), biotin, digoxigenin, or haptens and other entitieswhich can be made detectable. A label may be incorporated into nucleicacids and proteins at any position.

“Nucleic acid”, “oligonucleotide” or “polynucleotide” used herein maymean at least two nucleotides covalently linked together. The depictionof a single strand also defines the sequence of the complementarystrand. Thus, a nucleic acid also encompasses the complementary strandof a depicted single strand. Many variants of a nucleic acid may be usedfor the same purpose as a given nucleic acid. Thus, a nucleic acid alsoencompasses substantially identical nucleic acids and complementsthereof. A single strand provides a probe that may hybridize to thetarget sequence under stringent hybridization conditions. Thus, anucleic acid also encompasses a probe that hybridizes under stringenthybridization conditions.

Nucleic acids may be single stranded or double stranded, or may containportions of both double stranded and single stranded sequence. Thenucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, wherethe nucleic acid may contain combinations of deoxyribo- andribo-nucleotides, and combinations of bases including uracil, adenine,thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosineand isoguanine. Nucleic acids may be obtained by chemical synthesismethods or by recombinant methods.

A nucleic acid will generally contain phosphodiester bonds, althoughnucleic acid analogs may be included that may have at least onedifferent linkage, e.g., phosphoramidate, phosphorothioate,phosphorodithioate, or O-methylphosphoroamidite linkages and peptidenucleic acid backbones and linkages. Other analog nucleic acids includethose with positive backbones; non-ionic backbones, and non-ribosebackbones, including those described in U.S. Pat. Nos. 5,235,033 and5,034,506, which are incorporated by reference. Nucleic acids containingone or more non-naturally occurring or modified nucleotides are alsoincluded within one definition of nucleic acids. The modified nucleotideanalog may be located for example at the 5′-end and/or the 3′-end of thenucleic acid molecule. Representative examples of nucleotide analogs maybe selected from sugar- or backbone-modified ribonucleotides. It shouldbe noted, however, that also nucleobase-modified ribonucleotides, i.e.ribonucleotides, containing a non-naturally occurring nucleobase insteadof a naturally occurring nucleobase such as uridines or cytidinesmodified at the 5-position, e.g. 5-(2-amino)propyl uridine, 5-bromouridine; adenosines and guanosines modified at the 8-position, e.g.8-bromo guanosine; deaza nucleotides, e.g. 7-deaza-adenosine; O- andN-alkylated nucleotides, e.g. N6-methyl adenosine are suitable. The2′-OH-group may be replaced by a group selected from H, OR, R, halo, SH,SR, NH₂, NHR, NR₂ or CN, wherein R is C₁-C₆ alkyl, alkenyl or alkynyland halo is F, Cl, Br or I. The nucleic acid may comprise a 2′-ribosereplacement such as a 2′-O-methyl and 2′-fluoro group, as described inU.S. Pat. No. 7,138,517, the contents of which are incorporated hereinby reference. Modified nucleotides also include nucleotides conjugatedwith cholesterol through a hydroxyprolinol linkage as described inKrutzfeldt et al., Nature 438:685-689 (2005), Soutschek et al., Nature432:173-178 (2004), and U.S. Patent Publication No. 20050107325, whichare incorporated herein by reference. Modified nucleotides and nucleicacids may also include locked nucleic acids (LNA), as described in U.S.Pat. No. 20020115080, which is incorporated herein by reference.Additional modified nucleotides and nucleic acids are described in U.S.Patent Publication No. 20050182005, which is incorporated herein byreference. Modifications of the ribose-phosphate backbone may be donefor a variety of reasons, e.g., to increase the stability and half-lifeof such molecules in physiological environments or as probes on abiochip. Mixtures of naturally occurring nucleic acids and analogs maybe made; alternatively, mixtures of different nucleic acid analogs, andmixtures of naturally occurring nucleic acids and analogs may be made.

“Operably linked” used herein may mean that expression of a gene isunder the control of a promoter with which it is spatially connected. Apromoter may be positioned 5′ (upstream) or 3′ (downstream) of a geneunder its control. The distance between the promoter and the gene may beapproximately the same as the distance between that promoter and thegene it controls in the gene from which the promoter is derived. As isknown in the art, variation in this distance may be accommodated withoutloss of promoter function.

“Probe” as used herein may mean an oligonucleotide capable of binding toa target nucleic acid of complementary sequence through one or moretypes of chemical bonds, usually through complementary base pairing,usually through hydrogen bond formation. Probes may bind targetsequences lacking complete complementarity with the probe sequencedepending upon the stringency of the hybridization conditions. There maybe any number of base pair mismatches that will interfere withhybridization between the target sequence and a single stranded nucleicacid described herein. However, if the number of mismatches is so greatthat no hybridization can occur under even the least stringent ofhybridization conditions, the sequence is not a complementary targetsequence. A probe may be single stranded or partially single andpartially double stranded. The strandedness of the probe is dictated bythe structure, composition, and properties of the target sequence.Probes may be directly labeled or indirectly labeled such as with biotinto which a streptavidin complex may later bind.

“Promoter” as used herein may mean a synthetic or naturally-derivedmolecule which is capable of conferring, activating or enhancingexpression of a nucleic acid in a cell. A promoter may comprise one ormore specific regulatory elements to further enhance expression and/orto alter the spatial expression and/or temporal expression of same. Apromoter may also comprise distal enhancer or repressor elements, whichcan be located as much as several thousand base pairs from the startsite of transcription. A promoter may be derived from sources includingviral, bacterial, fungal, plants, insects, and animals. A promoter mayregulate the expression of a gene component constitutively ordifferentially with respect to cell, the tissue or organ in whichexpression occurs or, with respect to the developmental stage at whichexpression occurs, or in response to external stimuli such asphysiological stresses, pathogens, metal ions, or inducing agents.Representative examples of promoters include the bacteriophage 17promoter, bacteriophage T3 promoter, SP6 promoter, lacoperator-promoter, tac promoter, SV40 late promoter, SV40 earlypromoter, RSV-LTR promoter, CMV IE promoter, SV40 early promoter or SV40late promoter and the CMV IE promoter.

“Reducing the amount of virus replication” used herein may mean that thelevel or quantity of the target viral genome in the target cell isreduced by at least about 2-fold to 100-fold or more, as compared to acontrol, i.e., an identical target cell not treated according to thesubject methods.

“Selectable marker” used herein may mean any gene which confers aphenotype on a cell in which it is expressed to facilitate theidentification and/or selection of cells which are transfected ortransformed with a genetic construct. Representative examples ofselectable markers include the ampicillin-resistance gene (Amp^(r)),tetracycline-resistance gene (Tc^(r)), bacterial kanamycin-resistancegene (Kan^(r)), zeocin resistance gene, the AURI-C gene which confersresistance to the antibiotic aureobasidin A, phosphinothricin-resistancegene, neomycin phosphotransferase gene (nptII), hygromycin-resistancegene, beta-glucuronidase (GUS) gene, chloramphenicol acetyltransferase(CAT) gene, green fluorescent protein-encoding gene and luciferase gene.

“Stringent hybridization conditions” used herein may mean conditionsunder which a first nucleic acid sequence (e.g., probe) will hybridizeto a second nucleic acid sequence (e.g., target), such as in a complexmixture of nucleic acids. Stringent conditions are sequence-dependentand will be different in different circumstances. Generally, stringentconditions may be selected to be about 5-10° C. lower than the thermalmelting point (T_(m)) for the specific sequence at a defined ionicstrength pH. The T_(m) may be the temperature (under defined ionicstrength, pH, and nucleic concentration) at which 50% of the probescomplementary to the target hybridize to the target sequence atequilibrium (as the target sequences are present in excess, at T_(m),50% of the probes are occupied at equilibrium). Stringent conditions maybe those in which the salt concentration is less than about 1.0 M sodiumion, such as about 0.01-1.0 M sodium ion concentration (or other salts)at pH 7.0 to 8.3 and the temperature is at least about 30° C. for shortprobes (e.g., about 10-50 nucleotides) and at least about 60° C. forlong probes (e.g., greater than about 50 nucleotides). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide. For selective or specific hybridization, apositive signal may be at least 2 to 10 times background hybridization.Exemplary stringent hybridization conditions include the following: 50%formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS,incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.

“Substantially complementary” used herein may mean that a first sequenceis at least 60%-99% identical to the complement of a second sequenceover a region of 8-50 or more nucleotides, or that the two sequenceshybridize under stringent hybridization conditions. [0.066]“Substantially identical” used herein may mean that a first and secondsequence are at least 60%-99% identical over a region of 8-50 or morenucleotides or amino acids, or with respect to nucleic acids, if thefirst sequence is substantially complementary to the complement of thesecond sequence.

“Subject” used herein may mean a mammal, such as a human.

“Target” as used herein may mean a polynucleotide that may be bound byone or more probes under stringent hybridization conditions.

“Terminator” used herein may mean a sequence at the end of atranscriptional unit which signals termination of transcription. Aterminator may be a 3′-non-translated DNA sequence containing apolyadenylation signal, which may facilitate the addition ofpolyadenylate sequences to the 3′-end of a primary transcript. Aterminator may be derived from sources including viral, bacterial,fungal, plants, insects, and animals. Representative examples ofterminators include the SV40 polyadenylation signal, HSV TKpolyadenylation signal, CYC1 terminator, ADH terminator, SPA terminator,nopaline synthase (NOS) gene terminator of Agrobacterium tumefaciens,the terminator of the Cauliflower mosaic virus (CaMV) 35S gene, the zeingene terminator from Zea mays, the Rubisco small subunit gene (SSU) geneterminator sequences, subclover stunt virus (SCSV) gene sequenceterminators, rho-independent E. coli terminators, and the lacZ alphaterminator.

“Treat” or “treating” used herein when referring to protection of ananimal from a condition may mean preventing, suppressing, repressing, oreliminating the condition. Preventing the condition involvesadministering a composition described herein to an animal prior to onsetof the condition. Suppressing the condition involves administering thecomposition to an animal after induction of the condition but before itsclinical appearance. Repressing the condition involves administering thecomposition to an animal after clinical appearance of the condition suchthat the condition is reduced or prevented from worsening. Eliminationof the condition involves administering the composition to an animalafter clinical appearance of the condition such that the animal nolonger suffers from the condition.

“Therapeutically effective amount” used herein or “therapeuticallyefficient” as to a drug dosage may refer to dosage that provides thespecific pharmacological response for which the drug is administered ina significant number of subjects in need of such treatment. The“therapeutically effective amount” may vary according, for example, thephysical condition of the patient, the age of the patient and theseverity of the disease.

“Unit dosage form,” used herein may refer to a physically discrete unitsuitable as a unitary dosage for a human or animal subject. Each unitmay contain a predetermined quantity of a composition described herein,calculated in an amount sufficient to produce a desired effect inassociation with a pharmaceutically acceptable diluent, carrier orvehicle. The specifications for a unit dosage form may depend on theparticular composition employed and the effect to be achieved, and thepharmacodynamics associated with the composition in the host.

“Variant” used herein to refer to a nucleic acid may mean (i) a portionof a referenced nucleotide sequence; (ii) the complement of a referencednucleotide sequence or portion thereof; (iii) a nucleic acid that issubstantially identical to a referenced nucleic acid or the complementthereof; or (iv) a nucleic acid that hybridizes under stringentconditions to the referenced nucleic acid, complement thereof, or asequences substantially identical thereto.

“Vector” used herein may mean a nucleic acid sequence containing anorigin of replication. A vector may be a plasmid, bacteriophage,bacterial artificial chromosome or yeast artificial chromosome. A vectormay be a DNA or RNA vector. A vector may be either a self-replicatingextrachromosomal vector or a vector that integrates into a host genome.

“Wild type” used herein to refer to a sequence may mean a coding,non-coding or interface sequence that may be an allelic form of asequence that performs the natural or normal function for that sequence.Wild type sequences may include multiple allelic forms of a cognatesequence, for example, multiple alleles of a wild type sequence mayencode silent or conservative changes to the protein sequence that acoding sequence encodes.

2. MicroRNA

While not being bound by theory, a gene coding for a miRNA may betranscribed leading to production of an miRNA precursor known as thepri-miRNA. The pri-miRNA may be part of a polycistronic RNA comprisingmultiple pri-miRNAs. The pri-miRNA may form a hairpin with a stem andloop. The stem may comprise mismatched bases.

The hairpin structure of the pri-miRNA may be recognized by Drosha,which is an RNase III endonuclease. Drosha may recognize terminal loopsin the pri-miRNA and cleave approximately two helical turns into thestem to produce a 30 200 nt precursor known as the pre-miRNA. Drosha maycleave the pri-miRNA with a staggered cut typical of RNase IIIendonucleases yielding a pre-miRNA stem loop with a 5′ phosphate and -2nucleotide 3′ overhang. Approximately one helical turn of the stem (˜10nucleotides) extending beyond the Drosha cleavage site may be essentialfor efficient processing. The pre-miRNA may then be actively transportedfrom the nucleus to the cytoplasm by Ran-GTP and the export receptorEx-portin-5.

The pre-miRNA may be recognized by Dicer, which is also an RNase IIIendonuclease. Dicer may recognize the double-stranded stem of thepre-miRNA. Dicer may also recognize the 5′ phosphate and 3′ overhang atthe base of the stem loop. Dicer may cleave off the terminal loop twohelical turns away from the base of the stem loop leaving an additional5′ phosphate and ˜2 nucleotide 3′ overhang. The resulting siRNA-likeduplex, which may comprise mismatches, comprises the mature miRNA and asimilar-sized fragment known as the miRNA*. The miRNA and miRNA* may bederived from opposing arms of the pri-miRNA and pre-miRNA. MiRNA*sequences may be found in libraries of cloned miRNAs but typically atlower frequency than the miRNAs.

Although initially present as a double-stranded species with miRNA*, themiRNA may eventually become incorporated as a single-stranded RNA into aribonucleoprotein complex known as the RNA-induced silencing complex(RISC). Various proteins can form the RISC, which can lead tovariability in the specificity for miRNA/miRNA* duplexes, the bindingsite of the target gene, the activity of the miRNA (repress oractivate), and which strand of the miRNA/miRNA* duplex is loaded in tothe RISC.

When the miRNA strand of the miRNA:miRNA* duplex is loaded into theRISC, the miRNA* may be removed and degraded. The strand of themiRNA:miRNA* duplex that is loaded into the RISC may be the strand whose5′ end is less tightly paired. In cases where both ends of themiRNA:miRNA* have roughly equivalent 5′ pairing, both miRNA and miRNA*may have gene silencing activity.

The RISC may identify target nucleic acids based on high levels ofcomplementarity between the miRNA and the mRNA, especially bynucleotides 2-8 of the miRNA. Only one case has been reported in animalswhere the interaction between the miRNA and its target was along theentire length of the miRNA. This was shown for mir-196 and Hox B8 and itwas further shown that mir-196 mediates the cleavage of the Hox B8 mRNA(Yekta et al 2004, Science 304-594). Otherwise, such interactions areknown only in plants (Bartel & Bartel 2003, Plant Physiol 132-709).

A number of studies have looked at the base-pairing requirement betweenmiRNA and its mRNA target for achieving efficient inhibition oftranslation (reviewed by Bartel 2004, Cell 116-281). In mammalian cells,the first 8 nucleotides of the miRNA may be important (Doench & Sharp2004 GenesDev 2004-504). However, other parts of the microRNA may alsoparticipate in mRNA binding. Moreover, sufficient base pairing at the 3′end can compensate for insufficient pairing at the 5′ end (Brennecke etal, 2005 PLoS 3-e85). Computation studies, analyzing miRNA binding onwhole genomes have suggested a specific role for bases 2-7 at the 5′ endof the miRNA in target binding but the role of the first nucleotide,found usually to be “A” was also recognized (Lewis et at 2005 Cell120-15). Similarly, nucleotides 1-7 or 2-8 were used to identify andvalidate targets by Krek et al (2005, Nat Genet 37-495).

The target sites in the mRNA may be in the 5′ UTR, the 3′ UTR or in thecoding region. Interestingly, multiple miRNAs may regulate the same mRNAtarget by recognizing the same or multiple sites. The presence ofmultiple miRNA binding sites in most genetically identified targets mayindicate that the cooperative action of multiple RISCs provides the mostefficient translational inhibition.

MiRNAs may direct the RISC to downregulate gene expression by either oftwo mechanisms: mRNA cleavage or translational repression. The miRNA mayspecify cleavage of the mRNA if the mRNA has a certain degree ofcomplementarity to the miRNA. When a miRNA guides cleavage, the cut maybe between the nucleotides pairing to residues 10 and 11 of the miRNA.Alternatively, the miRNA may repress translation if the miRNA does nothave the requisite degree of complementarity to the miRNA. Translationalrepression may be more prevalent in animals since animals may have alower degree of complementarity between the miRNA and the binding site.

It should be noted that there may be variability in the 5′ and 3′ endsof any pair of miRNA and miRNA*. This variability may be due tovariability in the enzymatic processing of Drosha and Dicer with respectto the site of cleavage. Variability at the 5′ and 3′ ends of miRNA andmiRNA* may also be due to mismatches in the stem structures of thepri-miRNA and pre-miRNA. The mismatches of the stem strands may lead toa population of different hairpin structures. Variability in the stemstructures may also lead to variability in the products of cleavage byDrosha and Dicer.

3. Nucleic Acid

A nucleic acid is provided herein. The nucleic acid may comprise thesequence of any one of SEQ ID NOS: 1-15,527 or a variant thereof. Thevariant may be a complement of the referenced nucleotide sequence. Thevariant may also be a nucleotide sequence that is substantiallyidentical to the referenced nucleotide sequence or the complementthereof. The variant may also be a nucleotide sequence which hybridizesunder stringent conditions to the referenced nucleotide sequence,complements thereof, or nucleotide sequences substantially identicalthereto. The nucleic acid may have a length of at least 10-250nucleotides. The nucleic acid may comprise a modified base. The nucleicacid may be synthesized or expressed in a cell (in vitro or in vivo)using a synthetic gene described herein. The nucleic acid may besynthesized as a single strand molecule and hybridized to asubstantially complementary nucleic acid to form a duplex.

-   -   a. Nucleic acid complex

The nucleic acid may further comprise one or more of the following: apeptide, a protein, a RNA-DNA hybrid, an antibody, an antibody fragment,a Fab fragment, and an aptamer.

-   -   b. Pri-miRNA

The nucleic acid may comprise a sequence of a pri-miRNA or a variantthereof. The pri-miRNA sequence may comprise from 45-30,000, 50-25,000,100-20,000, 1,000-1,500 or 80-100 nucleotides. The sequence of thepri-miRNA may comprise a pre-miRNA, miRNA and miRNA*, as set forthherein, and variants thereof. The sequence of the pri-miRNA may comprisethe sequence of any one of SEQ ID NOS: 1-15,527 or a variant thereof.

The pri-miRNA may form a hairpin structure. The hairpin may comprisefirst and second nucleic acid sequence that are substantiallycomplementary. The first and second nucleic acid sequence may be from37-50 nucleotides. The first and second nucleic acid sequence may beseparated by a third sequence of from 8-12 nucleotides. The hairpinstructure may have a free energy less than −25 Kcal/mole as calculatedby the Vienna algorithm with default parameters, as described inHofacker et al., Monatshefte f. Chemie 125: 167-188 (1994), the contentsof which are incorporated herein. The hairpin may comprise a terminalloop of 4-20, 8-12 or 10 nucleotides. The pri-miRNA may comprise atleast 19% adenosine nucleotides, at least 16% cytosine nucleotides, atleast 23% thymine nucleotides and at least 19% guanine nucleotides.

-   -   c. Pre-miRNA

The nucleic acid may also comprise a sequence of a pre-miRNA or avariant thereof. The pre-miRNA sequence may comprise from 45-200, 60-80or 60-70 nucleotides. The sequence of the pre-miRNA may comprise a miRNAand a miRNA* as set forth herein. The sequence of the pre-miRNA may alsobe that of a pri-miRNA excluding from 0-160 nucleotides from the 5′ and3′ ends of the pri-miRNA. The sequence of the pre-miRNA may comprise thesequence of any one of SEQ ID NOS: 1-15,527 or a variant thereof.

-   -   d. MiRNA

The nucleic acid may also comprise a sequence of a miRNA (includingmiRNA*) or a variant thereof. The miRNA sequence may comprise from13-33, 18-24 or 21-23 nucleotides. The miRNA may also comprise a totalof at least 5-40 nucleotides. The sequence of the miRNA may be the first13-33 nucleotides of the pre-miRNA. The sequence of the miRNA may alsobe the last 13-33 nucleotides of the pre-miRNA. The sequence of themiRNA may be differentially expressed during a viral infection, and maycomprise the sequence of any one of SEQ ID NOS: 1-9,221, 15,366-15,392,15,516-15,527, or a variant thereof as indicated in Table 1 and Table 8.

TABLE 8 The host and viral microRNAs which were differentially expressedupon viral infection. MID HIDs microRNA name Organism 15,366 15,379hsa-miR-181a Homo sapiens 15,367 15,380 hsa-miR-193a Homo sapiens 15,36815,381 hsa-miR-107 Homo sapiens 15,369 15,382 hsa-miR-103 Homo sapiens15,370 15,383 hsa-miR-296 Homo sapiens 15,371 15,384 hsa-miR-574 Homosapiens 15,372 15,385 hsa-miR-210 Homo sapiens 15,373 15,386 hsa-miR-21Homo sapiens 15,374 15,387 RG_AMB_10594 Homo sapiens 15,375 15,388hsv1-miR-H1 Human herpesvirus 1 15,376 15,389 RG_HSV2_Pred13 Humanherpesvirus 2 15,392 15,377 15,389 RG_HSV2_8 Human herpesvirus 2 15,39215,378 15,390 RG_fluA12 Influenza A virus 15,391 MID: SEQ ID NO of themature microRNA sequence HIDs: SEQ ID NO(S) of the hairpin microRNAprecursor microRNA name: The miRBase registry Sanger 9.2 microRNA name,excluding cases in which the names begins with “RG”. In these cases thenames are internal miRNA names of Rosetta Genomics. Organism: ThemicroRNA organism.

-   -   e. Anti-miRNA

The nucleic acid may also comprise a sequence of an anti-miRNA that iscapable of blocking the activity of a miRNA or miRNA*, such as bybinding to the pri-miRNA, pre-miRNA, miRNA or miRNA* (e.g. antisense orRNA silencing), or by binding to the target binding site. The anti-miRNAmay comprise a total of 5-100 or 10-60 nucleotides. The anti-miRNA mayalso comprise a total of at least 5-40 nucleotides. The sequence of theanti-miRNA may comprise (a) at least 5 nucleotides that aresubstantially identical or complementary to the 5′ of a miRNA and atleast 5-12 nucleotides that are substantially complementary to theflanking regions of the target site from the 5′ end of the miRNA, or (b)at least 5-12 nucleotides that are substantially identical orcomplementary to the 3′ of a miRNA and at least 5 nucleotide that aresubstantially complementary to the flanking region of the target sitefrom the 3′ end of the miRNA. The sequence of the anti-miRNA maycomprise the complement of any one of SEQ ID NOS: 1-15,527 or a variantthereof.

-   -   f. Binding Site of Target

The nucleic acid may also comprise a sequence of a target microRNAbinding site, or a variant thereof. The target site sequence maycomprise a total of 5-100 or 10-60 nucleotides. The target site sequencemay also comprise a total of at least 5-63 nucleotides. The target sitesequence may comprise at least 5 nucleotides of the sequence of any oneof SEQ ID NOS: 9,222-15,365 and 15,393-15,515 as indicated in Tables 3and 9.

TABLE 9 The miRNAs and their predicted binding sites microRNA Targetgene BS SEQ Gene name MID Organism name ID NO Ontology ID hsa-miR-181a15,366 Homo sapiens BCL2 15,436 GO: 0006959 hsa-miR-181a 15,366 Homosapiens BCL2 15,436 GO: 0051607 hsa-miR-181a 15,366 Homo sapiens CARD1115,416 GO: 0050776 hsa-miR-181a 15,366 Homo sapiens CBLB 15,506 GO:0006955 hsa-miR-181a 15,366 Homo sapiens CCL8 15,477 GO: 0006955hsa-miR-181a 15,366 Homo sapiens CCL8 15,477 GO: 0009615 hsa-miR-181a15,366 Homo sapiens CD4 15,471 GO: 0006955 hsa-miR-181a 15,366 Homosapiens CD59 15,450 GO: 0006955 hsa-miR-181a 15,366 Homo sapiens CXCL515,419 GO: 0006955 hsa-miR-181a 15,366 Homo sapiens ETS1 15,499 GO:0006955 hsa-miR-181a 15,366 Homo sapiens FAS 15,502 GO: 0006955hsa-miR-181a 15,366 Homo sapiens GBP6 15,489 GO: 0006955 hsa-miR-181a15,366 Homo sapiens IFNA17 15,511 GO: 0009615 hsa-miR-181a 15,366 Homosapiens IL2 15,483 GO: 0006955 hsa-miR-181a 15,366 Homo sapiens LIF15,400 GO: 0006955 hsa-miR-181a 15,366 Homo sapiens MS4A1 15,494 GO:0006955 hsa-miR-181a 15,366 Homo sapiens MS4A1 15,497 GO: 0006955hsa-miR-181a 15,366 Homo sapiens OPRK1 15,425 GO: 0006955 hsa-miR-181a15,366 Homo sapiens POLA 15,453 GO: 0009615 hsa-miR-181a 15,366 Homosapiens SAMHD1 15,399 GO: 0006955 hsa-miR-181a 15,366 Homo sapiensSEMA3C 15,393 GO: 0006955 hsa-miR-181a 15,366 Homo sapiens TNF 15,428GO: 0006959 hsa-miR-181a 15,366 Homo sapiens TNF 15,428 GO: 0009615hsa-miR-181a 15,366 Homo sapiens TNFAIP1 15,455 GO: 0006955 hsa-miR-181a15,366 Homo sapiens TNFSF4 15,496 GO: 0006955 hsa-miR-193a 15,367 Homosapiens CD97 15,468 GO: 0006955 hsa-miR-193a 15,367 Homo sapiens TNFAIP115,495 GO: 0006955 hsa-miR-107 15,368 Homo sapiens ARL6IP2 15,446 GO:0006955 hsa-miR-107 15,368 Homo sapiens BST1 15,395 GO: 0006959hsa-miR-107 15,368 Homo sapiens CCL13 15,460 GO: 0006955 hsa-miR-10715,368 Homo sapiens EBI2 15,456 GO: 0006955 hsa-miR-107 15,368 Homosapiens FCGR2A 15,487 GO: 0006955 hsa-miR-107 15,368 Homo sapiens FCGR2B15,488 GO: 0006955 hsa-miR-107 15,368 Homo sapiens IFIT1L 15,426 GO:0006955 hsa-miR-107 15,368 Homo sapiens IFNAR1 15,516 GO: 0009615hsa-miR-107 15,368 Homo sapiens IL15 15,421 GO: 0006955 hsa-miR-10715,368 Homo sapiens IL16 15,447 GO: 0006955 hsa-miR-107 15,368 Homosapiens IL1RAP 15,402 GO: 0006955 hsa-miR-107 15,368 Homo sapiens MICB15,433 GO: 0006955 hsa-miR-107 15,368 Homo sapiens OAS3 15,444 GO:0006955 hsa-miR-107 15,368 Homo sapiens SPON2 15,462 GO: 0006955hsa-miR-107 15,368 Homo sapiens TNF 15,424 GO: 0006959 hsa-miR-10715,368 Homo sapiens TNF 15,424 GO: 0009615 hsa-miR-103 15,369 Homosapiens ARL6IP2 15,446 GO: 0006955 hsa-miR-103 15,369 Homo sapiens BST115,395 GO: 0006959 hsa-miR-103 15,369 Homo sapiens CCL13 15,460 GO:0006955 hsa-miR-103 15,369 Homo sapiens EBI2 15,456 GO: 0006955hsa-miR-103 15,369 Homo sapiens FCGR2A 15,487 GO: 0006955 hsa-miR-10315,369 Homo sapiens FCGR2B 15,488 GO: 0006955 hsa-miR-103 15,369 Homosapiens IFIT1L 15,426 GO: 0006955 hsa-miR-103 15,369 Homo sapiens IFNAR115,516 GO: 0009615 hsa-miR-103 15,369 Homo sapiens IL15 15,421 GO:0006955 hsa-miR-103 15,369 Homo sapiens IL16 15,447 GO: 0006955hsa-miR-103 15,369 Homo sapiens IL1RAP 15,402 GO: 0006955 hsa-miR-10315,369 Homo sapiens MICB 15,433 GO: 0006955 hsa-miR-103 15,369 Homosapiens OAS3 15,444 GO: 0006955 hsa-miR-103 15,369 Homo sapiens SPON215,462 GO: 0006955 hsa-miR-103 15,369 Homo sapiens TNF 15,424 GO:0006959 hsa-miR-103 15,369 Homo sapiens TNF 15,424 GO: 0009615hsa-miR-296 15,370 Homo sapiens CD22 15,397 GO: 0006955 hsa-miR-29615,370 Homo sapiens CD6 15,405 GO: 0006955 hsa-miR-296 15,370 Homosapiens CD6 15,440 GO: 0006955 hsa-miR-296 15,370 Homo sapiens CD8A15,466 GO: 0006955 hsa-miR-296 15,370 Homo sapiens CXCL10 15,501 GO:0006955 hsa-miR-296 15,370 Homo sapiens GBP4 15,490 GO: 0006955hsa-miR-296 15,370 Homo sapiens GCK 15,464 GO: 0006955 hsa-miR-29615,370 Homo sapiens HLA-DOA 15,415 GO: 0006955 hsa-miR-296 15,370 Homosapiens LAT2 15,396 GO: 0006955 hsa-miR-296 15,370 Homo sapiens LIF15,470 GO: 0006955 hsa-miR-296 15,370 Homo sapiens MAP4K2 15,439 GO:0006955 hsa-miR-296 15,370 Homo sapiens PVRL1 15,465 GO: 0006955hsa-miR-296 15,370 Homo sapiens SQSTM1 15,475 GO: 0006955 hsa-miR-29615,370 Homo sapiens TNFSF15 15,504 GO: 0006955 hsa-miR-296 15,370 Homosapiens VIPR1 15,458 GO: 0006955 hsa-miR-574 15,371 Homo sapiens IL28RA15,486 GO: 0050691 hsa-miR-210 15,372 Homo sapiens CD59 15,406 GO:0006955 hsa-miR-21 15,373 Homo sapiens CCL1 15,513 GO: 0006955hsa-miR-21 15,373 Homo sapiens CCL20 15,512 GO: 0006955 hsa-miR-2115,373 Homo sapiens CTSC 15,418 GO: 0006955 hsa-miR-21 15,373 Homosapiens FASLG 15,401 GO: 0006955 hsa-miR-21 15,373 Homo sapiens IL12A15,515 GO: 0006955 hsa-miR-21 15,373 Homo sapiens LILRB4 15,430 GO:0006955 hsa-miR-21 15,373 Homo sapiens PAG1 15,482 GO: 0006955hsa-miR-21 15,373 Homo sapiens ST6GAL1 15,484 GO: 0006959 AMB_1059415,374 Homo sapiens C5AR1 15,445 GO: 0006955 AMB_10594 15,374 Homosapiens CD74 15,461 GO: 0006955 AMB_10594 15,374 Homo sapiens CD79B15,437 GO: 0006955 AMB_10594 15,374 Homo sapiens CX3CL1 15,413 GO:0006955 AMB_10594 15,374 Homo sapiens DBNL 15,451 GO: 0006955 AMB_1059415,374 Homo sapiens HLA-DOA 15,435 GO: 0006955 AMB_10594 15,374 Homosapiens IFITM1 15,442 GO: 0006955 AMB_10594 15,374 Homo sapiens IL1R115,474 GO: 0006955 AMB_10594 15,374 Homo sapiens IL6ST 15,427 GO:0006955 AMB_10594 15,374 Homo sapiens MBP 15,443 GO: 0006955 AMB_1059415,374 Homo sapiens MS4A2 15,478 GO: 0006959 AMB_10594 15,374 Homosapiens NCR3 15,459 GO: 0006955 AMB_10594 15,374 Homo sapiens TNFSF815,414 GO: 0006955 AMB_10594 15,374 Homo sapiens TOLLIP 15,411 GO:0006955 hsv1-miR-H1 15,375 Human herpesvirus 1 ADA 15,448 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 ANXA11 15,409 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 CXCL9 15,473 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 HLA-DOB 15,469 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 IFIT5 15,423 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 OASL 15,412 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 POU2AF1 15,441 GO: 0006959hsv1-miR-H1 15,375 Human herpesvirus 1 PTGER4 15,420 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 SERPINB4 15,505 GO: 0006955hsv1-miR-H1 15,375 Human herpesvirus 1 SLA2 15,454 GO: 0050776hsv1-miR-H1 15,375 Human herpesvirus 1 ST6GAL1 15,422 GO: 0006959hsv1-miR-H1 15,375 Human herpesvirus 1 TCF1 15,498 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 CD24 15,480 GO: 0006959HSV2_Pred13 15,376 Human herpesvirus 2 IL16 15,493 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 IL1A 15,431 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 IL1RL1 15,434 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 MBP 15,507 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 OLR1 15,394 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 TNFAIP1 15,403 GO: 0006955HSV2_Pred13 15,376 Human herpesvirus 2 TRIM5 15,404 GO: 0009615HSV2_Pred13 15,376 Human herpesvirus 2 VIPR1 15,410 GO: 0006955 HSV2_815,377 Human herpesvirus 2 ABCE1 15,472 GO: 0009615 HSV2_8 15,377 Humanherpesvirus 2 CAST 15,514 GO: 0006955 HSV2_8 15,377 Human herpesvirus 2CCL20 15,429 GO: 0006955 HSV2_8 15,377 Human herpesvirus 2 CCR2 15,476GO: 0006955 HSV2_8 15,377 Human herpesvirus 2 CXCL3 15,417 GO: 0006955HSV2_8 15,377 Human herpesvirus 2 DUOX2 15,408 GO: 0009615 fluA12 15,378Influenza A virus C19orf2 15,479 GO: 0009615 fluA12 15,378 Influenza Avirus CAST 15,467 GO: 0006955 fluA12 15,378 Influenza A virus CBLB15,509 GO: 0006955 fluA12 15,378 Influenza A virus CCL8 15,438 GO:0006955 fluA12 15,378 Influenza A virus CCL8 15,438 GO: 0009615 fluA1215,378 Influenza A virus CCR9 15,432 GO: 0006955 fluA12 15,378 InfluenzaA virus CLEC6A 15,463 GO: 0006955 fluA12 15,378 Influenza A virus CTSS15,481 GO: 0006955 fluA12 15,378 Influenza A virus CXCL12 15,485 GO:0006955 fluA12 15,378 Influenza A virus CXCL12 15,485 GO: 0009615 fluA1215,378 Influenza A virus CXCL5 15,510 GO: 0006955 fluA12 15,378Influenza A virus CXCL6 15,500 GO: 0006955 fluA12 15,378 Influenza Avirus IFNGR2 15,451 GO: 0009615 fluA12 15,378 Influenza A virus IL1RAP15,508 GO: 0006955 fluA12 15,378 Influenza A virus MADCAM1 15,407 GO:0006955 fluA12 15,378 Influenza A virus MS4A1 15,492 GO: 0006955 fluA1215,378 Influenza A virus OAS3 15,457 GO: 0006955 fluA12 15,378 InfluenzaA virus SMAD3 15,503 GO: 0050776 fluA12 15,378 Influenza A virusTNFRSF11A 15,491 GO: 0006955 fluA12 15,378 Influenza A virus ZF 15,398GO: 0009615 microRNA name: The miRBase registry (Release 9.2) microRNAname, excluding cases in which the names begins with “RG”. In thesecases the names are internal miRNA names of Rosetta Genomics. MID: SEQID NO of the mature microRNA Target gene name: Target gene nameaccording to RefSeq database BS SEQ ID NO: The SEQ ID NO of the bindingsite of the microRNA to the 3′ UTR of the target gene. Gene Ontology ID:Gene Ontology (GO) ID. All are related to viral infection and to theimmune response, as described in Table 10.

TABLE 10 The description of Gene Ontology IDs GOid Description GO:0009615 response to virus GO: 0051607 defense response to virus GO:0050691 regulation of antiviral response by host GO: 0006959 humoralimmune response GO: 0006955 immune response GO: 0050776 regulation ofimmune response Description: The Gene Ontology description of GO ID

4. Synthetic Gene

A synthetic gene is also provided comprising a nucleic acid describedherein operably linked to a transcriptional and/or translationalregulatory sequence. The synthetic gene may be capable of modifying theexpression of a target gene with a binding site for a nucleic aciddescribed herein. Expression of the target gene may be modified in acell, tissue or organ. The synthetic gene may be synthesized or derivedfrom naturally-occurring genes by standard recombinant techniques. Thesynthetic gene may also comprise terminators at the 3′-end of thetranscriptional unit of the synthetic gene sequence. The synthetic genemay also comprise a selectable marker.

5. Vector

A vector is also provided comprising a nucleic acid described herein,such as a pri-miRNA, pre-miRNA, miRNA, anti-miRNA, target gene bindingsite, or synthetic gene. The vector may be an expression vector. Anexpression vector may comprise additional elements. For example, theexpression vector may have two replication systems allowing it to bemaintained in two organisms, e.g., in one host cell for expression andin a second host cell (e.g., bacteria) for cloning and amplification.For integrating expression vectors, the expression vector may contain atleast one sequence homologous to the host cell genome, and preferablytwo homologous sequences which flank the expression construct. Theintegrating vector may be directed to a specific locus in the host cellby selecting the appropriate homologous sequence for inclusion in thevector. The vector may also comprise a selectable marker gene to allowthe selection of transformed host cells.

6. Host Cell

A host cell is also provided comprising a vector, synthetic gene ornucleic acid described herein. The cell may be a bacterial, fungal,plant, insect or animal cell. For example, the host cell line may beDG44 and DUXB 11 (Chinese Hamster Ovary lines, DHFR minus), HELA (humancervical carcinoma), CVI (monkey kidney line), COS (a derivative of CVIwith SV40 T antigen), 81610 (Chinese hamster fibroblast) BALBC/3T3(mouse fibroblast), HAK (hamster kidney line), SP2/O (mouse myeloma),P3.times.63-Ag3.653 (mouse myeloma), BFA-1c1BPT (bovine endothelialcells), RAJI (human lymphocyte) and 293 (human kidney). Host cell linesmay be available from commercial services, the American Tissue CultureCollection or from published literature.

7. Probes

A probe is also provided comprising a nucleic acid described herein.Probes may be used for screening and diagnostic methods, as outlinedherein. The probe may be attached or immobilized to a solid substrate,such as a biochip.

The probe may have a length of from 8 to 500, 10 to 100 or 20 to 60nucleotides. The probe may also have a length of at least 8-300nucleotides. The probe may further comprise a linker sequence of from10-60 nucleotides.

8. Biochip

A biochip is also provided. The biochip may comprise a solid substratecomprising an attached probe or plurality of probes described herein.The probes may be capable of hybridizing to a target sequence understringent hybridization conditions. The probes may be attached atspatially defined addresses on the substrate. More than one probe pertarget sequence may be used, with either overlapping probes or probes todifferent sections of a particular target sequence. The probes may becapable of hybridizing to target sequences associated with a singledisorder. The probes may either be synthesized first, with subsequentattachment to the biochip, or may be directly synthesized on thebiochip.

The solid substrate may be a material that may be modified to containdiscrete individual sites appropriate for the attachment or associationof the probes and is amenable to at least one detection method.Representative examples of substrates include glass and modified orfunctionalized glass, plastics (including acrylics, polystyrene andcopolymers of styrene and other materials, polypropylene, polyethylene,polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon ornitrocellulose, resins, silica or silica-based materials includingsilicon and modified silicon, carbon, metals, inorganic glasses andplastics. The substrates may allow optical detection without appreciablyfluorescing.

The substrate may be planar, although other configurations of substratesmay be used as well. For example, probes may be placed on the insidesurface of a tube, for flow-through sample analysis to minimize samplevolume. Similarly, the substrate may be flexible, such as flexible foam,including closed cell foams made of particular plastics.

The biochip and the probe may be derivatized with chemical functionalgroups for subsequent attachment of the two. For example, the biochipmay be derivatized with a chemical functional group including, but notlimited to, amino groups, carboxyl groups, oxo groups or thiol groups.Using these functional groups, the probes may be attached usingfunctional groups on the probes either directly or indirectly using alinker. The probes may be attached to the solid support by either the 5′terminus, 3′ terminus, or via an internal nucleotide.

The probe may also be attached to the solid support non-covalently. Forexample, biotinylated oligonucleotides can be made, which may bind tosurfaces covalently coated with streptavidin, resulting in attachment.Alternatively, probes may be synthesized on the surface using techniquessuch as photopolymerization and photolithography.

9. miRNA Expression Analysis

A method of identifying miRNAs that are associated with disease or apathological condition, such as viral infection is also provided,comprising contacting a biological sample with a probe or biochipprovided herein and detecting the amount of hybridization. PCR may beused to amplify nucleic acids in the sample, which may provide highersensitivity. A bioinformatic method may be used to identify a specificmiRNA target or target pattern that is common among different viruses,and to identify a target of human miRNA in a viral genome. The methodmay be used in a system to identify a mRNA target of a host or viralmiRNA. The target may be useful to evaluate the role of a miRNA in avirus-host interaction by up or down regulation, or for the developmentof a therapeutic use of a miRNA.

The level of the nucleic acid in the sample may also be compared to acontrol sample (e.g., a normal cell) to determine whether the nucleicacid is differentially expressed (e.g., overexpressed orunderexpressed). The ability to identify miRNAs that are differentiallyexpressed in pathological cells compared to a control can providehigh-resolution, high-sensitivity datasets which may be used in theareas of diagnostics, prognostics, therapeutics, drug development,pharmacogenetics, biosensor development, and other related areas. Anexpression profile generated by the current methods may be a“fingerprint” of the state of the sample with respect to a number ofmiRNAs. While two states may have any particular miRNA similarlyexpressed, the evaluation of a number of miRNAs simultaneously allowsthe generation of a gene expression profile that is characteristic ofthe state of the cell. That is, normal tissue may be distinguished fromdiseased tissue. By comparing expression profiles of tissue in knowndifferent disease states, information regarding which miRNAs areassociated in each of these states may be obtained. Then, diagnosis maybe performed or confirmed to determine whether a tissue sample has theexpression profile of normal or disease tissue. This may provide formolecular diagnosis of related conditions.

10. Determining Expression Levels

The expression level of a viral infection- or disease-associated nucleicacid may be informative in a number of ways. For example, differentialexpression of a viral infection- or disease-associated nucleic acidcompared to a control may be diagnostic of a patient suffering from theviral infection or disease. Expression levels of a viral infection- ordisease-associated nucleic acid may also be used to monitor thetreatment and viral infection or disease state of a patient.Furthermore, expression levels of a viral infection- ordisease-associated miRNA may allow the screening of drug candidates foraltering a particular expression profile or suppressing an expressionprofile associated with viral infection or disease.

A target nucleic acid may be detected and levels of the target nucleicacid measured by contacting a sample comprising the target nucleic acidwith a biochip comprising an attached probe sufficiently complementaryto the target nucleic acid and detecting hybridization to the probeabove control levels.

The target nucleic acid may also be detected by immobilizing the nucleicacid to be examined on a solid support such as nylon membranes andhybridizing a labeled probe with the sample. Similarly, the targetnucleic may also be detected by immobilizing the labeled probe to asolid support and hybridizing a sample comprising a labeled targetnucleic acid. Following washing to remove the non-specifichybridization, the label may be detected.

The target nucleic acid may also be detected in situ by contactingpermeabilized cells or tissue samples with a labeled probe to allowhybridization with the target nucleic acid. Following washing to removethe non-specifically bound probe, the label may be detected.

These assays can be direct hybridization assays or can comprise sandwichassays, which include the use of multiple probes, as generally outlinedin U.S. Pat. Nos. 5,681,702; 5,597,909; 5,545,730; 5,594,117; 5,591,584;5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802; 5,635,352;5,594,118; 5,359,100; 5,124,246; and 5,681,697, each of which is herebyincorporated by reference.

A variety of hybridization conditions may be used, including high,moderate and low stringency conditions as outlined above. The assays maybe performed under stringency conditions which allow hybridization ofthe probe only to the target. Stringency can be controlled by altering astep parameter that is a thermodynamic variable, including, but notlimited to, temperature, formamide concentration, salt concentration,chaotropic salt concentration pH, or organic solvent concentration.

Hybridization reactions may be accomplished in a variety of ways.Components of the reaction may be added simultaneously, or sequentially,in different orders. In addition, the reaction may include a variety ofother reagents. These include salts, buffers, neutral proteins, e.g.,albumin, detergents, etc. which may be used to facilitate optimalhybridization and detection, and/or reduce non-specific or backgroundinteractions. Reagents that otherwise improve the efficiency of theassay, such as protease inhibitors, nuclease inhibitors andanti-microbial agents may also be used as appropriate, depending on thesample preparation methods and purity of the target.

11. Diagnostic

A method of diagnosis is also provided. The method comprises detecting adifferential expression level of a disease-associated nucleic acid in abiological sample. The sample may be derived from a patient. Diagnosisof a disease state in a patient may allow for prognosis and selection oftherapeutic strategy. Further, the developmental stage of cells may beclassified by determining temporarily expressed disease-associatednucleic acids.

In situ hybridization of labeled probes to tissue arrays may beperformed. When comparing the fingerprints between an individual and astandard, the skilled artisan can make a diagnosis, a prognosis, or aprediction based on the findings. It is further understood that thegenes which indicate the diagnosis may differ from those which indicatethe prognosis and molecular profiling of the condition of the cells maylead to distinctions between responsive or refractory conditions or maybe predictive of outcomes.

12. Drug Screening

A method of screening therapeutics is also provided. The methodcomprises contacting a pathological cell capable of expressing a diseaserelated nucleic acid with a candidate therapeutic and evaluating theeffect of a drug candidate on the expression profile of the diseaseassociated nucleic acid. Having identified the differentially expressednucleic acid, a variety of assays may be executed. Test compounds may bescreened for the ability to modulate gene expression of the diseaseassociated nucleic acid. Modulation includes both an increase and adecrease in gene expression.

The test compound or drug candidate may be any molecule, e.g., protein,oligopeptide, small organic molecule, polysaccharide, polynucleotide,etc., to be tested for the capacity to directly or indirectly alter thedisease phenotype or the expression of the disease associated nucleicacid. Drug candidates encompass numerous chemical classes, such as smallorganic molecules having a molecular weight of more than 100 and lessthan about 500, 1,000, 1,500, 2,000 or 2,500 daltons. Candidatecompounds may comprise functional groups necessary for structuralinteraction with proteins, particularly hydrogen bonding, and typicallyinclude at least an amine, carbonyl, hydroxyl or carboxyl group,preferably at least two of the functional chemical groups. The candidateagents may comprise cyclical carbon or heterocyclic structures and/oraromatic or polyaromatic structures substituted with one or more of theabove functional groups. Candidate agents are also found amongbiomolecules including peptides, saccharides, fatty acids, steroids,purines, pyrimidines, derivatives, structural analogs or combinationsthereof.

Combinatorial libraries of potential modulators may be screened for theability to bind to the disease associated nucleic acid or to modulatethe activity thereof. The combinatorial library may be a collection ofdiverse chemical compounds generated by either chemical synthesis orbiological synthesis by combining a number of chemical building blockssuch as reagents. Preparation and screening of combinatorial chemicallibraries is well known to those of skill in the art. Such combinatorialchemical libraries include, but are not limited to, peptide librariesencoded peptides, benzodiazepines, diversomers such as hydantoins,benzodiazepines and dipeptide, vinylogous polypeptides, analogousorganic syntheses of small compound libraries, oligocarbamates, and/orpeptidyl phosphonates, nucleic acid libraries, peptide nucleic acidlibraries, antibody libraries, carbohydrate libraries, and small organicmolecule libraries.

13. Gene Silencing

Also provided is a method of reducing the expression of a target gene ina cell, tissue or organ. Expression of the target gene may be reduced byexpressing a nucleic acid described herein that comprises a sequencesubstantially complementary to one or more binding sites of the targetmRNA. The nucleic acid may be a miRNA or a variant thereof. The nucleicacid may also be pri-miRNA, pre-miRNA, or a variant thereof, which maybe processed to yield a miRNA. The expressed miRNA may hybridize to asubstantially complementary binding site on the target mRNA, which maylead to activation of RISC-mediated gene silencing. An example for astudy employing over-expression of miRNA is provided in Yekta et al2004, Science 304-594, which is incorporated herein by reference. Thenucleic acids described herein may also be used to inhibit expression oftarget genes using antisense methods well known in the art, as well asRNAi methods described in U.S. Pat. Nos. 6,506,559 and 6,573,099, whichare incorporated by reference.

The target gene may be a viral gene, the level of which may be reducedby expressing a viral or human miRNA. The target gene may also be ahuman gene that is expressed upon viral infection, the level of whichmay be reduced by expressing a viral or human miRNA. The target of genesilencing may be a protein that causes the silencing of a secondprotein. By repressing expression of the target gene, expression of thesecond protein may be increased. Examples for efficient suppression ofmiRNA expression are the studies by Esau et al 2004 JBC 275-52361; andCheng et al 2005 Nucleic Acids Res. 33-1290, which is incorporatedherein by reference.

14. Gene Enhancement

Also provided is a method of increasing the expression of a target genein a cell, tissue or organ. Expression of the target gene may beincreased by expressing a nucleic acid described herein that comprises asequence substantially complementary to a pri-miRNA, pre-miRNA, miRNA ora variant thereof. The nucleic acid may be an anti-miRNA. The anti-miRNAmay hybridize with a pri-miRNA, pre-miRNA or miRNA, thereby reducing itsgene repression activity. Expression of the target gene may also beincreased by expressing a nucleic acid described herein that issubstantially complementary to a portion of the binding site in thetarget gene, such that binding of the nucleic acid to the binding sitemay prevent miRNA binding.

The target gene may be a viral gene, expression of which may reduceinfectivity of the virus. The target gene may also be a human gene,expression of which may reduce infectivity of the virus or increaseresistance or immunity to the viral infection.

15. Reducing Viral Replication

A method of reducing the amount of viral replication is provided, whichmay occur via gene silencing or gene enhancement using the nucleic aidas described herein. The nucleic acid may also be used to reduce theexpression of a target gene in a cell such as a viral gene in avirus-infected cell. Expression of the viral or target gene may bereduced by expressing the nucleic acid, which may comprise a sequencesubstantially complementary to one or more binding sites of the targetgene. The nucleic acid may be a miRNA or a variant thereof. The nucleicacid may also be a pri-miRNA, pre-miRNA, or a variant thereof, which maybe processed to yield a miRNA. The expressed miRNA may hybridize to asubstantially complementary binding site on the target mRNA, which maylead to interruption of the function of the gene. In the case of a viraltarget, replication of the virus may be inhibited, and the viralinfection may be reduced or eliminated.

The target gene may be a viral gene, which may be reduced by expressinga viral or human miRNA. The target gene may also be a human gene that isexpressed upon viral infection, which may be reduced by expressing aviral or human miRNA. The target of gene silencing may be a protein thatcauses the silencing of a second protein. By repressing expression ofthe target gene, expression of the second protein may be decreased.

16. Therapeutic

Also provided is a method of modulating a disease or disorder, which maybe associated with a viral infection. In general, the nucleic aciddescribed herein may be used as a modulator of the expression of a genethat is at least partially complementary to the nucleic acid. Further, amiRNA molecule may act as a target for a therapeutic screeningprocedure, e.g. inhibition or activation of a miRNA molecule mightmodulate a cellular differentiation process, e.g. apoptosis.

Furthermore, an existing miRNA molecule may be used as a startingmaterial for the manufacture of a sequence-modified miRNA molecule, inorder to modify the target-specificity thereof, e.g. an oncogene, amultidrug-resistance gene or another therapeutic target gene. Further, amiRNA molecule may be modified, so that it may be processed and thengenerated as double-stranded siRNA that may again be directed against atherapeutically relevant target. Furthermore, a miRNA molecule may beused for tissue reprogramming procedures, e.g. a differentiated cellline might be transformed by expression of a miRNA molecule into adifferent cell type or a stem cell.

17. Compositions

Also provided herein is a pharmaceutical composition, which may comprisea nucleic acid described herein and optionally a pharmaceuticallyacceptable carrier. The nucleic acid may be an active ingredient of thecomposition. The composition may be used for diagnostic or therapeuticapplications. The administration of the pharmaceutical composition maybe carried out by known methods, wherein a nucleic acid is introducedinto a desired target cell in vitro or in vivo.

The composition may be formulated in combination with appropriate,pharmaceutically acceptable carriers or diluents, and can be formulatedinto preparations in solid, semi-solid, liquid or gaseous forms, such astablets, capsules, powders, granules, ointments, solutions,suppositories, injections, inhalants and aerosols. As such,administration of the agents can be achieved in various ways, includingoral, buccal, rectal, parenteral, intraperitoneal, intradermal,transdermal, intracheal, etc.

18. Nucleic Acid Delivery

The nucleic acid may be introduced to a cell, tissue or organ in asingle- or double-stranded form or capable of being expressed by asynthetic gene using methods well known to those skilled in the art,including as described in U.S. Pat. No. 6,506,559 which is incorporatedby reference.

Methods for the delivery of nucleic acid molecules are described inAkhtar et al., (Trends Cell Bio. 2, 139, 1992). WO 94/02595 describesgeneral methods for delivery of RNA molecules. These protocols can beutilized for the delivery of virtually any nucleic acid molecule.Nucleic acid molecules can be administered to cells by a variety ofmethods known to those familiar to the art, including, but notrestricted to, encapsulation in liposomes, by iontophoresis, or byincorporation into other vehicles, such as hydrogels, cyclodextrins,biodegradable nanocapsules, and bioadhesive microspheres. Alternatively,the nucleic acid/vehicle combination is locally delivered by directinjection or by use of an infusion pump. Other routes of deliveryinclude, but are not limited to oral (tablet or pill form) and/orintrathecal delivery (Gold, 1997, Neuroscience, 76, 1153-1158). Otherapproaches include the use of various transport and carrier systems, forexample, through the use of conjugates and biodegradable polymers. Moredetailed descriptions of nucleic acid delivery and administration areprovided for example in WO93/23569, WO99/05094, and WO99/04819.

The nucleic acids can be introduced into tissues or host cells by anynumber of routes, including viral infection, microinjection, or fusionof vesicles. Jet injection may also be used for intra-muscularadministration, as described by Furth et al. (Anal Biochem 115205:365-368, 1992). The nucleic acids can be coated onto goldmicroparticles, and delivered intradermally by a particle bombardmentdevice, or “gene gun” as described in the literature (see, for example,Tang et al. Nature 356:152-154, 1992), where gold microprojectiles arecoated with the DNA, then bombarded into skin cells.

19. Kits

Also provided is a kit comprising a nucleic acid described hereintogether with any or all of the following: assay reagents, buffers,probes and/or primers, and sterile saline or another pharmaceuticallyacceptable emulsion and suspension base. In addition, the kit mayinclude instructional materials containing directions (e.g., protocols)for the practice of the methods described herein.

20. Virus

The methods and nucleic acids described herein may be associated withany one of a number of different visuses, including HSV1, HSV2, RSV,EBV, Influenza A, HCV, HPV, HIV, HBV, and Vaccinia. Influenza virusinfection is a major public health problem, causing millions of cases ofsevere illness and as many as 500,000 deaths each year worldwide (WHOreport, 2004, A56/23). Influenza virus has A, B and C types, among whichthe type A can be further classified into many sub-types according tothe variations in NA and HA genes. Thus far, there have been 15 HAsubtypes and 9 NA subtypes and the different combinations between HA andNA subtypes can form many types of influenza A virus subtypes.

Although inactivated vaccines are 60-80% effective against the matchedinfluenza strains, vaccination coverage is a problem worldwide.Moreover, this strategy provides no protection against unexpectedstrains. Currently, antiviral drugs are the best defense against theseoutbreaks, but they provide only partial protection (Nicholson, etc.,Lancet, 355:1845-1850, 2000), usually companied with some side effects,especially to the central nervous system (Wenzel, JAMA, 283:1057-1059,2000).

Epstein Barr Virus (EBV), a large DNA virus of the Herpes family thatinfects normal human B cells, is the etiologic agent of infectiousmononucleosis and is strongly associated with Burkitt's lymphoma andnasopharingal carcinoma.

Herpes simplex virus type-1 and 2 (HSV1 and HSV2) enter and reactivatefrom latency in sensory neurons, although the events governing theseprocesses are little understood. During latency, only thelatency-associated transcripts are produced.

21. Disease

The methods and nucleic acids described herein may be associated withany one of a number of different diseases, including Burkitt's lymphoma,nasopharingal carcinoma, ovarian carcinoma, cervical cancer, hepatitis,mononucleosis, influenza, genital herpes, encephalitis, andbronchiolitis.

EXAMPLES Example 1 Prediction Of MiRNAs

We surveyed a number of viral genomes for potential miRNA coding genesusing three computational approaches similar to those described in U.S.patent application Ser. Nos. 60/522,459, 10/709,577 and 10/709,572, thecontents of which are incorporated herein by reference, for predictingmiRNAs. The predicted hairpins and potential miRNAs were scored bythermodynamic stability, as well as structural and contextual features.The algorithm was calibrated by using miRNAs in the Sanger Databasewhich had been validated.

1. Viral Genome Screen

Table 1 and Table 8 list the SEQ ID NO for each predicted hairpin(“HID”) of a particular viral genome (“V”; See also Table 7). Table 1also lists the genomic location for each hairpin (“Hairpin_Loc”). Theformat for the genomic location is a concatenation of <strand><startposition>. For viruses that have more than one chromosome or segment,such as Influenza A, the segment number is identified in column “C”(viruses with only one chromosome have a value of 1 in this column). Thegenetic location is based on the NCBI—Entrez Nucleotides database. TheEntrez Nucleotides database is a collection of sequences from severalsources, including GenBank, RefSeq, and PDB. Table 7 shows the accessionnumber and the build (version) for each of the viral genomes used inthis screen. Two viruses in Table 7 have multiple accession numbersbecause each segment (i.e., chromosome analog) of the virus' genomes hada different accession number. One of the viruses has no accessionnumber.

Table 1 also lists the SEQ ID NO (“MID”) for each predicted miRNA andmiRNA*. Table 1 also lists the prediction score grade for each hairpin(“P”) on a scale of 0-1 (1 means that the hairpin is the most reliable),as described in Hofacker et al., Monatshefte f. Chemie 125: 167-188,1994. Table 1 also lists the p-value (“Pval”) calculated out ofbackground hairpins for the values of each P scores. All the p-valueswere significant, i.e., less than 0.05. If the Pval is indicated as 0.0,then the Pval is less than 0.0001. The p-values were calculated bycomparing the palgrade of the tested hairpin to the palgrade of othersequences without pre-selection of hairpins.

Table 1 also lists whether the miRNAs were validated by expressionanalysis (“E”) (Y=Yes, N=No), as detailed in Table 2. It should be notedthat failure to sequence or detect expression of a miRNA does notnecessarily mean that a miRNA does not exist. Such undetected miRNAs maybe expressed in tissues other than those tested. In addition, suchundetected miRNAs may be expressed in the test tissues, but at adifference stage or under different conditions compared to theexperimental cells.

Table 1 also lists a genetic location cluster (“LC”) for those hairpinsthat are within 1,000 nucleotides of each other of a particular virus.Each miRNA that has the same LC shares the same genetic cluster.Hairpins that overlap were not clustered.

Example 2 Prediction of Target Genes

The predicted miRNAs from the computational screen of Example 1 wereused to predict human and viral target genes and their binding sitesusing computational approaches for predicting miRNAs, similar toapproaches described in U.S. patent application Ser. Nos. 60/522,459,10/709,577 and 10/709,572, the contents of which are incorporated hereinby reference.

1. Human Genome Screen

-   -   a. Human Target Genes

Table 3 and Table 9 list a predicted human target gene for each miRNA(“MID”) from a particular virus (“V”) and its hairpin (“HID”) from theviral genome screen. The virus codes listed in “V” are, as for Table 1,defined in Table 7. The names of the target genes (“Target_Gene”) inTable 3 were taken from NCBI Reference Sequence release 9(http://www.ncbi.nlm.nih.gov; Pruitt et al., Nucleic Acids Res,33(1):D501-D504, 2005; Pruitt et al., Trends Genet., 16(1):44-47, 2000;and Tatusova et al., Bioinformatics, 15(7-8):536-43, 1999). Target geneswere identified by having a mammalian conserved perfect complementarymatch of a 7 nucleotide miRNA seed (positions 2-8) and an A on the UTR(total=8 nucleotides). For a discussion on identifying target genes, seeLewis et al., Cell, 120: 15-20, (2005). For a discussion of the seedbeing sufficient for binding of a miRNA to a UTR, see Lim Lau et al.,(Nature 2005) and Brenneck et al, (PLoS Biol 2005).

The binding site screen only considered the first 4000 nucleotides perUTR and considered the longest transcript when there were severaltranscripts per gene. The filtering reduced the total number oftranscripts from 23626 to 14239. Table 3 lists the SEQ ID NO for thepredicted binding sites (“Binding_site”) for each target gene. Thesequence of the binding site includes the 20 nucleotides 5′ and 3′ ofthe binding site as they are located on the spliced mRNA. In cases thatthe binding site is comprised from 2 exons, 20 nucleotides are includedfrom both 5′ and 3′ ends of both exons.

-   -   b. Viral Target Genes

Human Herpes virus 1 and 2 are related to any of several inflammatorydiseases caused by a herpesvirus and marked in one case by groups ofwatery blisters on the skin or mucous membranes (as of the mouth andlips) above the waist and in the other by such blisters on the genitals.Human herpesvirus 4 (Epstein-Barr virus) is capable of causinginfectious mononucleosis and is associated with Burkitt's lymphoma andnasopharyngeal carcinoma. HIV strains are related to Acquired ImmuneDeficiency Syndrome (AIDS). Hepatitis B and C viruses are capable ofcausing inflammation of the liver. Human papillomavirus is capable ofcausing cervical cancer, human respiratory syncytial virus (RSV) iscapable of causing respiratory disease, and Influenza A virus is capableof causing Influenza. Vaccinia virus has not been shown to be capable ofcausing disease in humans, and is usually used for the preparation ofvaccines.

Example 3 Validation of miRNAs

To confirm the hairpins and miRNAs predicted in Example 1, we detectedexpression in various tissues using the high-throughput microarrayssimilar to those described in U.S. patent application Ser. Nos.60/522,459, 10/709,577 and 10/709,572, the contents of which areincorporated herein by reference. For each predicted precursor miRNA,mature miRNAs derived from both stems of the hairpin were tested.

1. Expression Analysis

Table 2 shows the hairpins (“HID”) of the third prediction set that werevalidated by detecting expression of related miRNAs (“MID”) from aparticular virus (“V”), as well as a code for the tissue (“Tissue”) inwhich expression was detected. In cases where there was more than onescore from the same miRNA in the same tissue, only the miRNA with thehigher score is presented.

The tissue and disease codes are listed in Table 4 and Table 5,respectively. Table 6 shows the relationship between each gene and atleast one disease, enabling a miRNA described herein to be connected toa disease. Table 6 condenses data derived from OMIM and lists for eachgene the numeric code(s) of the disease(s) associated with the gene.

All the tissues disclosed give an indication of a viral disease. Thefact that significant expression of the virus was measured implies thatin this tissue it may be involve in a viral disease(s). For example, ifa miRNA from HIV is expressed in a T cell line it may have an effect onAIDS. Of course cell lines represent only subset of the features of atissue as its function in an organ however we can deduce from theexpression as it is measured in the cell line.

Table 2 also shows the chip expression score grade, which ranges from500 to 65000 (“S”). A threshold of 500 was used to eliminatenon-significant signals and the score was normalized by miRNA microarrayprobe signals from different experiments. Variations in the intensitiesof fluorescence material between experiments may be due to variabilityin RNA preparation or labeling efficiency. Normalization was performedbased on the assumption that the total amount of miRNAs in each samplewas relatively constant. First, the background signal was subtractedfrom the raw signal of each probe, where the background signal wasdefined as 400. Next, each miRNA probe signal was divided by the averagesignal of all miRNAs, multiplied by 10000 and added back the backgroundsignal of 400. Thus, by definition, the sum of all miRNA probe signalsin each experiment was 10400.

Table 2 also shows a statistical analysis of the normalized signal(“Spval”) calculated on the normalized score. For each miRNA, a relevantcontrol group was used out of the full predicted miRNA list. Each miRNAhad an internal control of probes with mismatches. The relevant controlgroup contained probes with similar C and G percentage (abs diff <5%) inorder to have a similar Tm. The probe signal P value is the ratio overthe relevant control group probes with the same or higher signals. Theresults were p-value ≦0.05 and the score was above 500. In those casesfor which the SPVa1 is listed as 0.0, the value is less than 0.0001.

2. Sequencing

To further validate the hairpins (“HID”) of the second prediction, anumber of miRNAs were validated by sequencing methods similar to thosedescribed in U.S. patent application Ser. Nos. 60/522,459, 10/709,577and 10/709,572, the contents of which are incorporated herein byreference.

3. Northern Blot Analysis

A group of miRNAs were validated by Northern blot analysis, as shown inFIGS. 6, 9 and 10.

Example 4 Preparation of RNA libraries from Virus-Infected Cells andfrom Interferon A Treated Cells

RNA libraries from virus-infected cells were prepared. For each libraryfrom infected cells, a control library from uninfected cells was alsoprepared. Total RNA was extracted from the paired cell lines (infectedand uninfected) and labeled directly with either Cy5 or Cy3 (mirVanaTMmiRNA Labeling Kit, Ambion). Each set (labeled with either Cy3 or Cy5)was tested on the same micro-array slide of microRNAs (MIRDICATOR™,Rosetta Genomics).

RNA libraries were prepared from the following cell lines and viruses:

-   -   a. Primary human fibroblasts (HF, from amnion synthesis), human        neuroblastoma cell line (UKF NB4), and Vero cells, infected with        HSV1 or HSV2, including libraries of early stage and late stage        of infection for both viruses.    -   b. HEp2 cells infected with Respiratory Syncytial Virus (RSV).    -   c. MDCK cells (dog cells) infected with Influenza A (FluA).    -   In each case a library was also prepared from an uninfected        control of the same cell line.

RNA libraries were also prepared from interferon a treated cells andfrom untreated cells to evaluate the effect of interferon a on microRNAproduction.

MIRDICATOR™ microRNA array were used to detect novel host and viralencoded miRNAs in the libraries (phase-1).

Glass slides were printed with probes of all the known hsa-mirs inanti-sense (AS) orientation; as well as various positive and negativecontrols (e.g. U6). In addition, AS probes to the predictions ofmicroRNAs of viral genes were included. The predicted viral-microRNAsthat were probed and analyzed were: HSV1, HSV2, RSV, and FluA microRNAs.Therefore, for single hybridization, two sets of positive signals on themicroRNA array were obtained: expression of host (human) microRNAs andexpression of viral microRNAs, in infected versus uninfected cells.

Example 5 Use of MIRDICATOR™ microRNA Array to Detect RSV Induced miRNAs

Total RNA was extracted from HEp2 cells infected with RSV or fromcontrol non-infected HEp2 cells and labeled with cy3 and cy5. The probeswere hybridized together to the same microRNA array slide. The resultsdepict signals for all microRNAs for both probes plotted against eachother.

FIG. 1 shows the results of RSV infected and uninfected HEp2 cellshybridized on microRNA array. The human microRNA RG_AMB_(—)10594 (SEQ IDNO: 15,374) was significantly upregulated in the RSV infected HEp2 cellsas compared to uninfected control cells. The results suggest that hostmicroRNAs may play a role in RSV replication.

Example 6 Use of MIRDICATOR™ to Detect FluA Encoded microRNAs

MDCK cells were infected with FluA and control cells were leftuninfected. Three days after infection RNA was extracted, labeled withCy3 and Cy5 and hybridized to the glass-microRNA array.

The results shown in FIGS. 2A-2B as a plot of MDCK cells infected withFluA vs. uninfected cells. Two independent experiments are shown. Out of12 FluA probes (predicted by the bioinformatics-algorithm and spotted onthe microRNA array), one, FluA-12 (SEQ ID NO: 15,378), gave a positivesignal as shown circled in FIGS. 2A-2B. This viral-microRNA is validatedby real time PCR for microRNAs (MIR-PCR, see details of the procedurebelow).

Example 7 Use of MIRDICATOR™ to Detect HSV-1& HSV-2 Encoded microRNAs

Neuroblastoma, Vero cells (cell line from green monkey's kidney) andhuman fibroblasts (HF) were infected with either HSV-1 or HSV-2. RNAswere extracted and labeled with cy3 and cy5. Eighteen samples from Verocells and human fibroblasts (HF) were hybridized together to the sametype of microRNA array slide. Each set of samples were either uninfectedor infected with HSV-1 or with HSV-2. The results depict signals for allmicroRNAs from both probes, plotted against each other.

As shown in FIG. 3, the expression of hsv1-miR-H1 (SEQ ID NO: 15,375)was found in the late stage of HSV-1 infected Vero cells.

Two novel microRNAs of HSV-2: hsv2-8 (SEQ ID NO: 15,377) and hsv2-predl3(SEQ ID NO: 15,376) were found to be expressed in HSV2-infected Verocells as shown in FIG. 4, and to a lesser extent in human neuroblastomacell (UKF-NB4). These microRNAs are originated from the 3′ arm and the5′ arm of the same pre-microRNA and are found twice in the HSV-2 genome.The HSV-2 microRNAs were found to be expressed at the late stage ofinfection. These are the first validated two microRNAs of HSV-2, a maincause of genital herpes. The data was confirmed further by MIR-PCR (FIG.7) and by Northern blot analyses (FIGS. 9-10).

Example 8 Use of microRNA Array miRdicator™ to Detect Host microRNADifferential Expression During Viral Infections

Up and down regulation of host microRNA (Homo sapiens, hsa-mirs) duringviral infections could be observed in several infected cell lines. MDCKcells were infected with FluA. An uninfected control was included. Threedays after infection RNA was extracted, labeled with Cy3 and Cy5 andhybridized to the glass-microRNA array.

Table 11 depicts differential expression of host microRNAs that arecommon to Homo sapiens and MDCK in FluA infected cells. The results areaverage of two experiments. These results are further validated bymiRNA-RT-PCR and Northern blots.

Host hsa-miR-181a expression (SEQ ID NO: 15,366), is reduced not only inFluA infected MDCK cells, but also in RSV infected HEp2 cells (seeNorthern blot analysis in FIG. 6). The results of the microRNA array forhsa-miR-296 (SEQ ID NO: 15,370), hsa-miR-210 (SEQ ID NO: 15,372),hsa-miR-193a (SEQ ID NO: 15,367), hsa-miR-181a, hsa-miR-107 (SEQ ID NO:15,368) and hsa-miR-103 (SEQ ID NO: 15,369) by Northern blot and miR-PCRanalysis are under validation.

TABLE 11 Differential expression of host miRs in MDCK cells infectedwith FluA Signal from Signal from infected uninfected Fold probe sourcecells cells change comments hsa_miR_296 2674.5 435.5 (+)6 up-regulatedin infected cells hsa_miR_210 461 1746 (−)3.8 down-regulated in infectedcells hsa_miR_193a 2116.5 11879 (−)5.6 down-regulated in infected cellshsa_miR_181a 1880.5 10124 (−)5.4 down-regulated in infected cellshsa_miR_107 1160 6898 (−)5.9 down-regulated in infected cellshsa_miR_103 661 4243 (−)6.4 down-regulated in infected cells

Example 9 Higher Expression of Human hsa-miR-21 in Vero Cells Infectedwith HSV1 in Comparison to Vero Cells Infected with HSV2

Following infection of Vero cells with HSV-1 and HSV-2, RNA wasextracted, labeled with Cy3 and Cy5 and hybridized to the glass-microRNAarray. As demonstrated in

FIG. 8, hsa-miR-21 (SEQ ID NO: 15,373) is expressed at higher levels inVero cells infected with HSV-1 in comparison to Vero cells infected withHSV2.

Example 10 Expression of Host miRNA AMB-10594 in Viral Infected orInterferon Treated Cells

The following tests were carried out: interferon a treated humanfibroblasts (HF), HSV-1 and HSV-2 infected HF cells, and RSV infectedHep2 cells. All tests included an untreated or uninfected control. Threedays after interferon a treatment or viral infection RNA was extracted,labeled with Cy3 and Cy5 and hybridized to the glass-microRNA array. Asshown in FIG. 5, increased expression of host-miR AMB-10594 (SEQ ID NO:15,374) (shown circled) was found in: interferon treated HF cells (FIG.5C), HSV1 infected HF cells (FIG. 5D), HSV2 infected HF cells (FIG. 5B),and RSV infected HEp2 cells (FIG. 5A). In each of the graphs thetreated/infected cells are plotted against the untreated/uninfectedcells.

Example 11

Validation of the Results of the Microarray screening by Northern BlotAnalysis and by Cloning of Mirnas from Libraries of Virus Infected andCytokines Treated Cells

The results obtained from the microarray analysis were validated in twoprocedures:

I. Northern blot analysis. Northern blot analysis comparing RSV infectedHEp2 cells with uninfected HEp2 cells was performed. 5Oug of RNA/slotwere subjected to acrylamide-gel electrophoresis. Northern blot analysiswas performed using a P³²-labeled-AS-probe to human hsa-miR-181a. Theresult shown in FIG. 6 indicates the down-regulation of the host miR inthe RSV infected cells, thus confirming the microarray results.

II. Real time PCR, aimed at amplification of miRs (miR-PCR), adoptedfrom Shi and Chiang, (Biotechniques, 2005. 39(4): p. 519-25). As littleas 100 pg total RNA is polyadenylated and reverse-transcribed with apoly(T) adapter into cDNAs for real-time PCR using the miR-specificforward primer and the sequence complementary to the poly(T) adapter asthe reverse primer. This real-time PCR method is simple and sensitivefor quantifying the expression of miRs and also reveals miRtissue-specific expression patterns that cannot be resolved by Northernblot analysis.

Analysis by miR-PCR demonstrated specific expression of the two novelHSV2 miRs (HSV2-miR-8 (SEQ ID NO: 15,377) and HSV2-mir-pred13 (SEQ IDNO: 15,376) in HSV2 infected neuroblastoma (UKF-NB4) and Vero cells.Total RNA was extracted from infected cells, polyadenylated andreverse-transcribed with a poly(T) adapter into cDNAs. The results areshown in FIG. 7: miR-specific forward primer HSV2-miR-8 (FIG. 7A and7B), HSV2-miR-pred13 (FIG. 7A) or bulge-primer (FIG. 7B). The reverseprimer used was the sequence complementary to the poly(T) adapter. Theproducts were subjected to agarose gel electrophoresis to determinetheir relative size. Nonspecific bands formed the same pattern inuninfected and HSV1 infected cells.

The results of the miR-PCR revealed a bulge probe (as expected), ahigher band of about 100 nucleotides corresponding to the pre-microRNAprecursor of these miRs (FIG. 7).

For Northern blot analysis, total RNA was extracted from either Verocells or human neuroblastoma cells (UKF-NB4): uninfected, and HSV-1 andHSV-2 infected. The samples were enriched for small RNAs (Ambion kit).The small RNAs samples were run on Urea gel, 10 μg/lane, blotted toNitrocellulose and hybridized with ³²P labeled probe to HSV2-mir-pred-13or with ³²P labeled probe to HSV2-mir-8 (SEQ ID NO: 15,377). As shown inFIG. 9, after exposure of 30 days the precursor (˜100 nts) ofHSV2-mir-pred-13 (15,376) was visible. As shown in FIG. 10, theprecursor of HSV2-mir-8 (˜100 nts) was visible and in UKF-NB4, a band atthe region of ˜22 nts was also detected. The hybridization was specificto HSV2; no signal was detected under the same conditions with eitheruninfected cells or cell infected with HSV1. Experiments with specificinhibitors to these HSV2 miRs will help to determine their role in HSV-2infection.

Example 12 Epstain Barr-Virus (EBV) microRNAs are DifferentiallyExpressed and Can Block the Viral Replication

The EBV virus encodes several distinct miRNAs in latently infected cellsthat are located in two main clusters. The BART miRNAs (SEQ ID NOs:15,516, 15,520, 15,522, 15,524 and 15,526) are expressed at high levelsin stages I and II of latency, whereas the BHRF1 miRNAs (e.g. SEQ ID NO:15,518) are expressed at high levels in stage III latency, while beingessentially undetectable in other stages of virus life cycle. Inductionof lytic EBV replication in B95-8 cells, by Cisplatin and12-O-tetradecanonoyl phorbol-13-acetate (TPA) with n-Butyric acid or byTET ON/OFF regulated expression of immediate early (1E) gene ZEBRA(BZLF1), resulted in high expression of one of theBHRF-1-microRNA-cluster. This cluster is localized on the 5′ and 3′-UTRsof BHRF1 mRNA. ZEBRA, is IE key gene in EBV switch to lytic infection.EBV replication resulted in LMP-1 (latency associated protein 1)reduction and increased viral load as determined by FACS and RT-PCR.

B95-8 cells persistently infected with EBV were transfected with variousantagonists (2-O-Methyl antimir oligonucleotides, SEQ ID NOs: 15,517,15,519, 15,521, 15,523, 15,525, and 15,527) to EBV microRNAs. After 120hrs, cells were harvested, DNA was extracted, and EBV DNA copies/ml wasdetermined by qRTPCR, using commercial standards for EBV viral load(FIG. 11).

BHRF-1, a viral homologue to Bcl2 oncogene, is also a member of the IEproteins of EBV. Antisense blockage of BHRF1-miRNA expression resultedin increased number of viral particles, up to ten fold, in comparison toGFP control nonspecific antisense treatment (FIG. 11).

Anti-microRNA to BART-2 had a moderate effect on viral replication (FIG.11). Taken together, the result supports the notion that microRNAs playa central role in the control of viral life cycle and that theirsuppression leads to lytic activation and escape from latency. Thesefindings also indicate the potential use of microRNAs as bases forantiviral therapies.

Over expression of BHRF1-miRNA is achieved by transfection ofoligonucleotide mimicking the BHRF-1 microRNA into B-95-8 cells, usingserial dilutions. The oligonucleotides are comprised of two smallsynthetic RNA molecules with 5′-phophorylation(5′-/phos/rUrArUrCrUrUrUrUrGrCrGrGrCrArGrArArArUrUrGrA-3′ (SEQ ID NO:4,581); and 5′-/phos/rArArArUrUrCrUrGrUrUrGrCrArGrCrArGrArUrArGrC) (SEQID NO: 15,518), hybridized to each other. Immediately after transfectionand at 24 hrs intervals the transfected cells are harvested and EBVviral load is tested by RT-PCR.

Differential expression of EBV-mir-BHRF 1-2* (SEQ ID NO: 15,518) istested in B-95-8, before and after induction with doxycycline treatmentwhich initiates viral early cycles. RNA is extracted from the treatedand untreated cells for Northern blot analysis.

Example 13 Testing the Effect of HSV2 microRNAs on HSV2 Replication

Neuroblastoma and Vero cells that are stably transfected with a plasmidcontaining the preMicrRNA of HSV2 (the precursor of HSV2-mir 8 andHSV2-mir-pred13, SEQ ID NOs: 15,389 and 15,392), cloned underIE-CMV-promoter in pEGFP-N1, Clontech), are infected with either HSV1 orHSV2 to test the specific effect of over expression of these two HSV2microRNAs on HSV2 replication. Cells transfected with pEGFP-N1 emptyvector and cells transfected with a vector containing the premicroRNA inAS-orientation are used as negative controls. Northern blot analysis iscarried out to confirm that the construct produces the desiredHSV-2-mirs and viral load is tested by RT-PCR to evaluate the effect ofover expression of HSV-microRNAs on viral replication.

LENGTHY TABLES The patent application contains a lengthy table section.A copy of the table is available in electronic form from the USPTO website(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20160002639A1).An electronic copy of the table will also be available from the USPTOupon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

1-6. (canceled)
 7. A method of preventing or treating viral infection ora condition associated with a viral infection in a subject in needthereof comprising administering to the subject an effective amount of acomposition comprising a nucleic acid sequence selected from the groupconsisting of SEQ ID NOS: 1-9,221, 15,366-15,392 and 15,516-15,527; acomplementary sequence thereof; and a sequence at least about 80%identical thereto.
 8. The method of claim ₇, wherein the viral infectionis selected from the group consisting of HSV1, HSV2, RSV, EBV, InfluenzaA, HCV, HPV, HIV, HBV and Vaccinia virus infection.
 9. A method ofinhibiting expression of a target gene in a cell comprising introducinga nucleic acid into the cell in an amount sufficient to inhibitexpression of the target gene, wherein the target gene comprises abinding site substantially identical to a binding site as set forth inany one of SEQ ID NOS: 9,222-15,365, 15,393-15,515; and wherein thenucleic acid is a nucleic acid selected from the group consisting of SEQID NOS: 1-9,221, 15,366-15,392, and 15,516-15,527; a complementarysequence thereof; and a sequence at least about 80% identical thereto.10-18. (canceled)
 19. A method of reducing the amount of virusreplication in a target cell, said method comprising: introducing into atarget cell infected with the virus an effective amount of a compositioncomprising a nucleic acid sequence selected from the group consisting ofSEQ ID NOS: 1-9,221, 15,366-15,392 and 15,516-15,527; a complementarysequence thereof; and a sequence at least about 80% identical thereto.20. The method of claim 19, wherein said target cell is in vitro. 21.The method of claim 19, wherein said target cell is in vivo.
 22. Themethod of claim 21, wherein said method comprises administering thecomposition to a subject comprising said target cell.
 23. The method ofclaim 19, wherein said virus is selected from the group consisting ofHSVi, HSV2, RSV, EBV, Influenza A, HCV, HPV, HIV, HBV and Vaccinia. 24.The method of claim 19, wherein said method comprises treating saidsubject for viral mediated disease condition.
 25. The method of claim24, wherein said disease condition is selected from the group consistingof Burkitt's lymphoma, nasopharingal carcinoma, ovarian carcinoma,cervical cancer, hepatitis, mononucleosis, influenza, genital herpes,encephalitis, and bronchiolitis.